"Wrong" is in the eye of the beholder -- the same album name can be associated with different releases over time and in different countries, having differing numbers of tracks and/or different track orders. Granted, it is annoying when MPFreaker applies track numbers from different releases when working on tracks from the same album in your collection -- this is something that MPFreaker can definitely do better in the future. You can minimize this problem by ensuring that you have "Deep search" turned off.

As for changing existing track numbers, previous versions of MPFreaker would consider track numbers lacking a "track count" (e.g. "4" instead of "4/12") as fair game to overwrite even without the "Overwrite" feature turned on, with the rationale that the track information was incomplete. By popular demand, that has changed with version 1.8.4 and so MPFreaker should not do this anymore, requiring the "Overwrite" switch turned on to make any change to existing track values.